RiceVarMap2

Detailed information for vg0141375315:

Variant ID: vg0141375315 (JBrowse)

Variation Type: INDEL

Chromosome: chr01

Position: 41375315

Reference Allele: CT

Alternative Allele: C

Primary Allele: CT

Secondary Allele: C

Inferred Ancestral Allele : CT (evidence from allele frequency in Oryza rufipogon: CT: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TCATCGGGTCCCTCGTGTCCATCCCTACAGGTAATATATATGCAGATATATTTTGATCCACCAGTTTACACGCCAGGAATTAAACCATGCAGAACACATA[CT/C]
AACACATTTGATTTGCATGGCTGCATGCGCGCATTGATCGTCGATCAACATTCAACAGCAGTGCGATCCATCGGCGTGTGCAACGGCATATTGGGGAACA

Reverse complement sequence

TGTTCCCCAATATGCCGTTGCACACGCCGATGGATCGCACTGCTGTTGAATGTTGATCGACGATCAATGCGCGCATGCAGCCATGCAAATCAAATGTGTT[AG/G]
TATGTGTTCTGCATGGTTTAATTCCTGGCGTGTAAACTGGTGGATCAAAATATATCTGCATATATATTACCTGTAGGGATGGACACGAGGGACCCGATGA

Allele Frequencies:

Populations	Population Size	Frequency of CT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.20%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Populations

Population Size

Frequency of CT(primary allele)

Frequency of C(secondary allele)

Frequency of N

Frequency of DEL

Frequency of others Allele

All

4726

99.80%

0.20%

0.00%